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- PDB-9cea: Crystal structure of HP1alpha chromoshadow domain -

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Basic information

Entry
Database: PDB / ID: 9cea
TitleCrystal structure of HP1alpha chromoshadow domain
ComponentsChromobox protein homolog 5
KeywordsTRANSCRIPTION / HP1a / CSD domain
Function / homology
Function and homology information


chromocenter / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / ribonucleoprotein complex binding / heterochromatin / pericentric heterochromatin / : / transcription repressor complex ...chromocenter / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / ribonucleoprotein complex binding / heterochromatin / pericentric heterochromatin / : / transcription repressor complex / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by KRAB-ZFP proteins / kinetochore / histone deacetylase binding / nuclear envelope / heterochromatin formation / Factors involved in megakaryocyte development and platelet production / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / chromosome, telomeric region / ribonucleoprotein complex / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily
Similarity search - Domain/homology
Chromobox protein homolog 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSelvam, K. / Gaurav, N. / Kutateladze, T.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: The HP1 box of KAP1 organizes HP1 alpha for silencing of endogenous retroviral elements in embryonic stem cells.
Authors: Gaurav, N. / O'Hara, R. / Hyder, U. / Qin, W. / Her, C. / Romero, H. / Kumar, A. / Marcaida, M.J. / Singh, R.K. / Hovius, R. / Selvam, K. / Liu, J. / Martire, S. / Yao, Y. / Challa, A. / Dal ...Authors: Gaurav, N. / O'Hara, R. / Hyder, U. / Qin, W. / Her, C. / Romero, H. / Kumar, A. / Marcaida, M.J. / Singh, R.K. / Hovius, R. / Selvam, K. / Liu, J. / Martire, S. / Yao, Y. / Challa, A. / Dal Peraro, M. / Fierz, B. / Kono, H. / Cardoso, M.C. / Debelouchina, G.T. / Leonhardt, H. / D'Orso, I. / Banaszynski, L.A. / Kutateladze, T.G.
History
DepositionJun 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 5
B: Chromobox protein homolog 5
C: Chromobox protein homolog 5
D: Chromobox protein homolog 5


Theoretical massNumber of molelcules
Total (without water)28,8894
Polymers28,8894
Non-polymers00
Water1,928107
1
A: Chromobox protein homolog 5
B: Chromobox protein homolog 5


Theoretical massNumber of molelcules
Total (without water)14,4452
Polymers14,4452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-8 kcal/mol
Surface area7170 Å2
MethodPISA
2
C: Chromobox protein homolog 5
D: Chromobox protein homolog 5


Theoretical massNumber of molelcules
Total (without water)14,4452
Polymers14,4452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-8 kcal/mol
Surface area7290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.758, 66.854, 70.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Chromobox protein homolog 5 / Antigen p25 / Heterochromatin protein 1 homolog alpha / HP1 alpha


Mass: 7222.320 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX5, HP1A / Production host: Escherichia coli (E. coli) / References: UniProt: P45973
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7, 0.2 M sodium chloride and 20% w/v PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Aug 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→46.18 Å / Num. obs: 17068 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.055 / Rrim(I) all: 0.14 / Χ2: 1.04 / Net I/σ(I): 11.3
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.916 / Num. unique obs: 1446 / CC1/2: 0.652 / Rpim(I) all: 0.4 / Rrim(I) all: 1 / Χ2: 1.07

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→46.18 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / SU B: 6.54 / SU ML: 0.167 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27732 772 4.5 %RANDOM
Rwork0.22735 ---
obs0.22982 16249 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.082 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0 Å2-0 Å2
2---1.65 Å20 Å2
3---2.6 Å2
Refinement stepCycle: 1 / Resolution: 2.15→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 0 107 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121914
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161837
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.8412582
X-RAY DIFFRACTIONr_angle_other_deg0.6741.7814237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8225241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.894510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85610342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1030.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022220
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7613.979970
X-RAY DIFFRACTIONr_mcbond_other4.743.98970
X-RAY DIFFRACTIONr_mcangle_it7.0267.0991206
X-RAY DIFFRACTIONr_mcangle_other7.0237.1071207
X-RAY DIFFRACTIONr_scbond_it5.6174.278944
X-RAY DIFFRACTIONr_scbond_other5.6144.285945
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0327.7161376
X-RAY DIFFRACTIONr_long_range_B_refined9.93237.732047
X-RAY DIFFRACTIONr_long_range_B_other9.92937.752043
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 52 -
Rwork0.262 1172 -
obs--99.92 %

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